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libsbml.ListOfCompartmentGlyphs Class Reference
Inheritance diagram for libsbml.ListOfCompartmentGlyphs:
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Detailed Description

{layout}

layout Implementation of the ListOfCompartmentGlyphs construct from the “layout” package.

The ListOfCompartmentGlyphs is a container for the CompartmentGlyph elements of a Layout.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
CompartmentGlyph

Public Member Functions

def __len__
 
def addCVTerm
 
def append
 
def appendAndOwn
 
def appendAnnotation
 
def appendFrom
 
def appendNotes
 
def clear
 
def clone
 
def disablePackage
 
def enablePackage
 
def get
 
def getAncestorOfType
 
def getAnnotation
 
def getAnnotationString
 
def getColumn
 
def getCVTerm
 
def getCVTerms
 
def getElementByMetaId
 
def getElementBySId
 
def getElementName
 
def getItemTypeCode
 
def getLevel
 
def getLine
 
def getListOfAllElements
 
def getListOfAllElementsFromPlugins
 
def getMetaId
 
def getModel
 
def getModelHistory
 
def getNamespaces
 
def getNotes
 
def getNotesString
 
def getNumCVTerms
 
def getNumPlugins
 
def getPackageName
 
def getPackageVersion
 
def getParentSBMLObject
 
def getPlugin
 
def getPrefix
 
def getResourceBiologicalQualifier
 
def getResourceModelQualifier
 
def getSBMLDocument
 
def getSBOTerm
 
def getSBOTermAsURL
 
def getSBOTermID
 
def getTypeCode
 
def getURI
 
def getVersion
 
def hasValidLevelVersionNamespaceCombination
 
def insert
 
def insertAndOwn
 
def isPackageEnabled
 
def isPackageURIEnabled
 
def isPkgEnabled
 
def isPkgURIEnabled
 
def isSetAnnotation
 
def isSetMetaId
 
def isSetModelHistory
 
def isSetNotes
 
def isSetSBOTerm
 
def matchesRequiredSBMLNamespacesForAddition
 
def matchesSBMLNamespaces
 
def remove
 
def removeFromParentAndDelete
 
def removeTopLevelAnnotationElement
 
def renameMetaIdRefs
 
def renameSIdRefs
 
def renameUnitSIdRefs
 
def replaceTopLevelAnnotationElement
 
def setAnnotation
 
def setMetaId
 
def setModelHistory
 
def setNamespaces
 
def setNotes
 
def setSBOTerm
 
def size
 
def toSBML
 
def toXML
 
def toXMLNode
 
def unsetAnnotation
 
def unsetCVTerms
 
def unsetId
 
def unsetMetaId
 
def unsetModelHistory
 
def unsetName
 
def unsetNotes
 
def unsetSBOTerm
 

Member Function Documentation

def libsbml.ListOf.__len__ (   self)
inherited

Python method signature(s):

__len__(ListOf self)   int
def libsbml.SBase.addCVTerm (   self,
  args 
)
inherited

Python method signature(s):

addCVTerm(SBase self, CVTerm term, bool newBag=False)   int
addCVTerm(SBase self, CVTerm term)   int

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.ListOf.append (   self,
  args 
)
inherited

Python method signature(s):

append(ListOf self, SBase item)   int

Adds an item to the end of this ListOf's list of items.

This method makes a clone of the item handed to it. This means that when the ListOf object is destroyed, the original items will not be destroyed. For a method with an alternative ownership behavior, see the ListOf.appendAndOwn() method.

Parameters
itemthe item to be added to the list.
See also
appendAndOwn()
appendFrom()
def libsbml.ListOf.appendAndOwn (   self,
  args 
)
inherited

Python method signature(s):

appendAndOwn(ListOf self, SBase item)   int

Adds an item to the end of this ListOf's list of items.

This method does not clone the item handed to it; instead, it assumes ownership of it. This means that when the ListOf is destroyed, the item will be destroyed along with it. For a method with an alternative ownership behavior, see the ListOf.append() method.

Parameters
itemthe item to be added to the list.
See also
append()
appendFrom()
def libsbml.SBase.appendAnnotation (   self,
  args 
)
inherited

Python method signature(s):

appendAnnotation(SBase self, XMLNode annotation)   int
appendAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendAnnotation(XMLNode annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
appendAnnotation(string annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.ListOf.appendFrom (   self,
  args 
)
inherited

Python method signature(s):

appendFrom(ListOf self, ListOf list)   int

Adds a clone of a list of items to this ListOf's list.

Note that because this clones the objects handed to it, the original items will not be destroyed when this ListOf object is destroyed.

Parameters
lista list of items to be added.
See also
append()
appendAndOwn()
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

Python method signature(s):

appendNotes(SBase self, XMLNode notes)   int
appendNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.ListOf.clear (   self,
  doDelete = True 
)
inherited

Python method signature(s):

clear(ListOf self, bool doDelete=True)
clear(ListOf self)

Removes all items in this ListOf object.

If parameter doDelete is True (default), all items in this ListOf object are deleted and cleared, and thus the caller doesn't have to delete those items. Otherwise, all items are cleared only from this ListOf object; the caller is still responsible for deleting all items. (In the latter case, callers are advised to store pointers to all items elsewhere before calling this function.)

Parameters
doDeleteif True (default), all items are deleted and cleared. Otherwise, all items are just cleared and not deleted.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.ListOfCompartmentGlyphs.clone (   self)

{layout}

layout Implementation of the ListOfCompartmentGlyphs construct from the “layout” package.

The ListOfCompartmentGlyphs is a container for the CompartmentGlyph elements of a Layout.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
CompartmentGlyph Python method signature(s):
clone(ListOfCompartmentGlyphs self)   ListOfCompartmentGlyphs

Creates and returns a deep copy of this ListOfCompartmentGlyphs.

Returns
a (deep) copy of this ListOfCompartmentGlyphs.
def libsbml.SBase.disablePackage (   self,
  args 
)
inherited

Python method signature(s):

disablePackage(SBase self, string pkgURI, string pkgPrefix)   int

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

import sys
import os.path
from libsbml import *

# We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML('sbml-file-with-comp-elements.xml');

# We extract one of the species from the model we just read in.
s1 = doc.getModel().getSpecies(0);

# We construct a new model.  This model does not use the 'comp' package.
newDoc = SBMLDocument(3, 1);
newModel = newDoc.createModel();

# The following would fail with an error, because addSpecies() would
# first check that the parent of the given object has namespaces
# declared, and will discover that s1 does but newModel does not.

# newModel.addSpecies(s1);

# However, if we disable the 'comp' package on s1, then the call
# to addSpecies will work.

s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1',
          'comp');
newModel.addSpecies(s1);
Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
enablePackage()
def libsbml.SBase.enablePackage (   self,
  args 
)
inherited

Python method signature(s):

enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)   int

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether to enable (True) or disable (False) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
disablePackage()
def libsbml.ListOfCompartmentGlyphs.get (   self,
  args 
)

Python method signature(s):

get(ListOfCompartmentGlyphs self, long n)   CompartmentGlyph
get(ListOfCompartmentGlyphs self, long n)   CompartmentGlyph
get(ListOfCompartmentGlyphs self, string sid)   CompartmentGlyph
get(ListOfCompartmentGlyphs self, string sid)   CompartmentGlyph

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
get(long n)

Get a CompartmentGlyph from the ListOfCompartmentGlyphs.

Parameters
nthe index number of the CompartmentGlyph to get.
Returns
the nth CompartmentGlyph in this ListOfCompartmentGlyphs.
See also
size()

Method variant with the following signature:
get(string sid)

Get a CompartmentGlyph from the ListOfCompartmentGlyphs based on its identifier.

Parameters
sida string representing the identifier of the CompartmentGlyph to get.
Returns
CompartmentGlyph in this ListOfCompartmentGlyphs with the given sid or None if no such CompartmentGlyph exists.
See also
get()
size()
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

Python method signature(s):

getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase
getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

Python method signature(s):

getAnnotation(SBase self)   XMLNode
getAnnotation(SBase self)   XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getAnnotationString (   self,
  args 
)
inherited

Python method signature(s):

getAnnotationString(SBase self)   string
getAnnotationString(SBase self)   string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getColumn (   self)
inherited

Python method signature(s):

getColumn(SBase self)   long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
def libsbml.SBase.getCVTerm (   self,
  args 
)
inherited

Python method signature(s):

getCVTerm(SBase self, long n)   CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
def libsbml.SBase.getCVTerms (   self)
inherited

Python method signature(s):

getCVTerms()   CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns the CVTermList for this SBase.

def libsbml.ListOf.getElementByMetaId (   self,
  args 
)
inherited

Python method signature(s):

getElementByMetaId(ListOf self, string metaid)   SBase

Returns the first child element found with the given metaid.

Parameters
metaidstring representing the metaid of objects to find
Returns
the first element found with the given metaid, or None if no such object is found.
def libsbml.ListOf.getElementBySId (   self,
  args 
)
inherited

Python method signature(s):

getElementBySId(ListOf self, string id)   SBase

Returns the first child element found that has the given identifier.

This method searches this ListOf's list of items for SBML objects based on their 'id' attribute value in the model-wide SId namespace.

Parameters
idstring representing the id of objects to find.
Returns
the first element found with the given id, or None if no such object is found.
def libsbml.ListOfCompartmentGlyphs.getElementName (   self)

Python method signature(s):

getElementName(ListOfCompartmentGlyphs self)   string

Returns the XML element name of this SBML object.

def libsbml.ListOfCompartmentGlyphs.getItemTypeCode (   self)

Python method signature(s):

getItemTypeCode(ListOfCompartmentGlyphs self)   int

Returns the libSBML type code for the SBML objects contained in this ListOf object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters “SBML_”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for objects contained in this list: SBML_LAYOUT_COMPARTMENTGLYPH (default).
See also
getElementName()
getPackageName()
def libsbml.SBase.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBase self)   long

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

Python method signature(s):

getLine(SBase self)   long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
def libsbml.SBase.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.SBase.getListOfAllElementsFromPlugins (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElementsFromPlugins(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects contained in SBML package plugins.

This method walks down the list of all packages used by the model and returns all objects contained in them.

Returns
an SBaseList of all children objects from plugins.
def libsbml.SBase.getMetaId (   self)
inherited

Python method signature(s):

getMetaId(SBase self)   string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId()
def libsbml.SBase.getModel (   self)
inherited

Python method signature(s):

getModel(SBase self)   Model

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
def libsbml.SBase.getModelHistory (   self,
  args 
)
inherited

Python method signature(s):

getModelHistory(SBase self)   ModelHistory
getModelHistory(SBase self)   ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or None if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.getNamespaces (   self)
inherited

Python method signature(s):

getNamespaces(SBase self)   XMLNamespaces

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object, or None in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()
def libsbml.SBase.getNotes (   self,
  args 
)
inherited

Python method signature(s):

getNotes(SBase self)   XMLNode
getNotes(SBase self)   XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNotesString (   self,
  args 
)
inherited

Python method signature(s):

getNotesString(SBase self)   string
getNotesString(SBase self)   string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNumCVTerms (   self)
inherited

Python method signature(s):

getNumCVTerms(SBase self)   long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
def libsbml.SBase.getNumPlugins (   self)
inherited

Python method signature(s):

getNumPlugins(SBase self)   long

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
def libsbml.SBase.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBase self)   string

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
def libsbml.SBase.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(SBase self)   long

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
def libsbml.SBase.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBase self)   SBase
getParentSBMLObject(SBase self)   SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
def libsbml.SBase.getPlugin (   self,
  args 
)
inherited

Python method signature(s):

getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getPlugin(long n)

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:
getPlugin(string package)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
def libsbml.SBase.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBase self)   string

Returns the namespace prefix of this element.

def libsbml.SBase.getResourceBiologicalQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceBiologicalQualifier(SBase self, string resource)   long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getResourceModelQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceModelQualifier(SBase self, string resource)   long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBase self)   SBMLDocument
getSBMLDocument(SBase self)   SBMLDocument

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
def libsbml.SBase.getSBOTerm (   self)
inherited

Python method signature(s):

getSBOTerm(SBase self)   int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
def libsbml.SBase.getSBOTermAsURL (   self)
inherited

Python method signature(s):

getSBOTermAsURL(SBase self)   string

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

Python method signature(s):

getSBOTermID(SBase self)   string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.ListOf.getTypeCode (   self)
inherited

Python method signature(s):

getTypeCode(ListOf self)   int

Returns the libSBML type code for this object, namely, SBML_LIST_OF.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters “SBML_”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_LIST_OF (default).
Note
The various ListOf classes mostly differ from each other in what they contain. Hence, one must call getItemTypeCode() to fully determine the class of this SBML object.
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
getItemTypeCode()
getElementName()
getPackageName()
def libsbml.SBase.getURI (   self)
inherited

Python method signature(s):

getURI(SBase self)   string

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.

Returns
the URI of this element
See also
getSBMLDocument()
getPackageName()
def libsbml.SBase.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBase self)   long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

Python method signature(s):

hasValidLevelVersionNamespaceCombination(SBase self)   bool
def libsbml.ListOf.insert (   self,
  args 
)
inherited

Python method signature(s):

insert(ListOf self, int location, SBase item)   int

Inserts an item at a given position in this ListOf's list of items.

This variant of the method makes a clone of the item handed to it. This means that when the ListOf is destroyed, the original items will not be destroyed. For an alternative method with different ownership behavior, see insertAndOwn(int location, SBase item).

Parameters
locationthe location in the list where to insert the item.
itemthe item to be inserted to the list.
See also
insertAndOwn()
def libsbml.ListOf.insertAndOwn (   self,
  args 
)
inherited

Python method signature(s):

insertAndOwn(ListOf self, int location, SBase item)   int

Inserts an item at a given position in this ListOf's list of items.

This variant of the method makes a clone of the item handet to it. This means that when the ListOf is destroyed, the original items will not be destroyed.

Parameters
locationthe location where to insert the item
itemthe item to be inserted to the list
See also
insert()
def libsbml.SBase.isPackageEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
def libsbml.SBase.isPkgEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
def libsbml.SBase.isSetAnnotation (   self)
inherited

Python method signature(s):

isSetAnnotation(SBase self)   bool

Predicate returning True if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
True if a 'annotation' subelement exists, False otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.isSetMetaId (   self)
inherited

Python method signature(s):

isSetMetaId(SBase self)   bool

Predicate returning True if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See also
getMetaId()
setMetaId()
def libsbml.SBase.isSetModelHistory (   self)
inherited

Python method signature(s):

isSetModelHistory(SBase self)   bool

Predicate returning True if this object has a ModelHistory object attached to it.

Returns
True if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.isSetNotes (   self)
inherited

Python method signature(s):

isSetNotes(SBase self)   bool

Predicate returning True if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
True if a 'notes' subelement exists, False otherwise.
See also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.isSetSBOTerm (   self)
inherited

Python method signature(s):

isSetSBOTerm(SBase self)   bool

Predicate returning True if this object's 'sboTerm' attribute is set.

Returns
True if the 'sboTerm' attribute of this SBML object is set, False otherwise.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

Python method signature(s):

matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

Python method signature(s):

matchesSBMLNamespaces(SBase self, SBase sb)   bool
matchesSBMLNamespaces(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.
def libsbml.ListOfCompartmentGlyphs.remove (   self,
  args 
)

Python method signature(s):

remove(ListOfCompartmentGlyphs self, long n)   CompartmentGlyph
remove(ListOfCompartmentGlyphs self, string sid)   CompartmentGlyph

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
remove(long n)

Removes the nth item from this ListOfCompartmentGlyphs items and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters
nthe index of the item to remove
See also
size()

Method variant with the following signature:
remove(string sid)

Removes item in this ListOfCompartmentGlyphs items with the given identifier.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then None is returned.

Parameters
sidthe identifier of the item to remove
Returns
the item removed. As mentioned above, the caller owns the returned item.
def libsbml.ListOf.removeFromParentAndDelete (   self)
inherited

Python method signature(s):

removeFromParentAndDelete(ListOf self)   int

Because ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else.

If a particular ListOf subclass does indeed exist as a pointer only, this function will need to be overridden.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.removeTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)   int
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")   int
removeTopLevelAnnotationElement(SBase self, string elementName)   int

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.renameMetaIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameMetaIdRefs(SBase self, string oldid, string newid)

Renames all the meta-identifier attributes on this element.

In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameSIdRefs(SBase self, string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRefin Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameUnitSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameUnitSIdRefs(SBase self, string oldid, string newid)

Renames all the UnitSIdRef attributes on this element.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.replaceTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)   int
replaceTopLevelAnnotationElement(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
replaceTopLevelAnnotationElement(XMLNode annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()

Method variant with the following signature:
replaceTopLevelAnnotationElement(string annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.setAnnotation (   self,
  args 
)
inherited

Python method signature(s):

setAnnotation(SBase self, XMLNode annotation)   int
setAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.setMetaId (   self,
  args 
)
inherited

Python method signature(s):

setMetaId(SBase self, string metaid)   int

Sets the value of the meta-identifier attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
def libsbml.SBase.setModelHistory (   self,
  args 
)
inherited

Python method signature(s):

setModelHistory(SBase self, ModelHistory history)   int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.setNamespaces (   self,
  args 
)
inherited

Python method signature(s):

setNamespaces(SBase self, XMLNamespaces xmlns)   int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setNotes (   self,
  args 
)
inherited

Python method signature(s):

setNotes(SBase self, XMLNode notes)   int
setNotes(SBase self, string notes, bool addXHTMLMarkup=False)   int
setNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setNotes(string notes, bool addXHTMLMarkup = false)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

Python method signature(s):

setSBOTerm(SBase self, int value)   int
setSBOTerm(SBase self, string sboid)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()

Method variant with the following signature:
setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()
def libsbml.ListOf.size (   self)
inherited

Python method signature(s):

size(ListOf self)   long

Returns number of items in this ListOf list.

Returns
the number of items in this ListOf items.
def libsbml.SBase.toSBML (   self)
inherited

Python method signature(s):

toSBML(SBase self)   string *

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
def libsbml.ListOfCompartmentGlyphs.toXML (   self)

Python method signature(s):

toXML(ListOfCompartmentGlyphs self)   XMLNode

Creates an XMLNode object from this.

def libsbml.SBase.toXMLNode (   self)
inherited

Python method signature(s):

toXMLNode(SBase self)   XMLNode

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
def libsbml.SBase.unsetAnnotation (   self)
inherited

Python method signature(s):

unsetAnnotation(SBase self)   int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
def libsbml.SBase.unsetCVTerms (   self)
inherited

Python method signature(s):

unsetCVTerms(SBase self)   int

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetId (   self)
inherited

Python method signature(s):

unsetId(SBase self)   int

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetMetaId (   self)
inherited

Python method signature(s):

unsetMetaId(SBase self)   int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetModelHistory (   self)
inherited

Python method signature(s):

unsetModelHistory(SBase self)   int

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.unsetName (   self)
inherited

Python method signature(s):

unsetName(SBase self)   int

Unsets the value of the 'name' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetNotes (   self)
inherited

Python method signature(s):

unsetNotes(SBase self)   int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.unsetSBOTerm (   self)
inherited

Python method signature(s):

unsetSBOTerm(SBase self)   int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are: